Trends in SML intertidal data

What species are in the rocky intertidal data?

Let’s Plot Trends

Here are some functions we’ll apply to each species. I’ll then fit mixed models with all of them using

COUNT ~ YEAR * SITE + (1|TRANSECT)

with a gaussian error. Note, it’s count, so, I could use Poisson, but, that needs to be way more tuned to each model - this should be fine for a first cut?

Here’s how we’ll do it:

tseries_plot <- function(data){
  
  ggplot(data,
         aes(y = Count, x = Year,
             color = Transect)) +
    stat_summary(fun.data = mean_se) +
    stat_summary(fun.data = mean_se, geom = "line") +
    labs(color = "Transect", 
         y = "Count per sq m ± SE",  x = "Year")
}

tseries_fun <- function(data){
  glmmTMB(Count ~ Year + (1|Transect),
               data = data,
               family = gaussian)
  
}

generate_output <- function(data){
  cat(paste0("## ", data$Organism[1], " ", data$Organism[1], "  \n<br>"))
  
  tseries_plot(data) %>% print()
  
  # tseries_fun(adf) %>% 
  #   car::Anova(test.statistic  = "Chisq") %>% 
  #   tidy() %>%
  #   knitr::kable("html", digits = 3) %>% 
  #   kableExtra::kable_styling() %>%
  #   print
  # 
  cat("\n\n")
}

Now let’s purrr::walk() through the whole shebang.

walk(split(data, data$Organism), generate_output)

Acoela Acoela

Amphipoda Amphipoda

Annelid Annelid

Anomia simplex Anomia simplex

Anurida maritima Anurida maritima

Aplidium Aplidium

Asterias forbesi Asterias forbesi

Asterias rubens Asterias rubens

Astyris lunata Astyris lunata

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

Cancer Cancer

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

Cancer borealis Cancer borealis

Cancer irroratus Cancer irroratus

Carcinus maenus Carcinus maenus

Cerianthus Cerianthus

Cirratulus Cirratulus

Colus stimpsoni Colus stimpsoni

copepods copepods

Coryphella Coryphella

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

Crepidula fornicata Crepidula fornicata

Crisia eburna Crisia eburna

Culicoides Culicoides

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

Dendrodoa Dendrodoa

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

Dendronotus Dendronotus

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

Diadumene lineata Diadumene lineata

Euplana Euplana

Flustrellidra hispida Flustrellidra hispida

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

Foviella Foviella

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

Gammarid Gammarid

Halacarus Halacarus

Halichondria Halichondria

Hemigrapsus sanguineus Hemigrapsus sanguineus

Henricia sanguinolenta Henricia sanguinolenta

Hiatella arctica Hiatella arctica

Hippothoa hyalina Hippothoa hyalina

Idotea balthica Idotea balthica

Idotea baltica Idotea baltica

Isopods Isopods

Lacuna vincta Lacuna vincta

Lepidonotus Lepidonotus

Littorina littorea Littorina littorea

Littorina obtusata Littorina obtusata

Littorina obtusata (egg case) Littorina obtusata (egg case)

Littorina saxatilis Littorina saxatilis

Lycastopsis Lycastopsis

Metridium senile Metridium senile

Micrura affinis Micrura affinis

Modiolus modiolus Modiolus modiolus

Molgula Molgula

Mussel Mussel

Mya arenaria Mya arenaria

Mytilus edulis Mytilus edulis

Nematodes Nematodes

Nemertean Nemertean

Nicolea Nicolea

Notoplana Notoplana

Nucella lapillus Nucella lapillus

Nucella lapillus (egg case) Nucella lapillus (egg case)

Nudibranchia Nudibranchia

Oligochaete Oligochaete

Onchidoris Onchidoris

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

Ophiopholis Ophiopholis

Ostrea edulis Ostrea edulis

Pagurus acadianus Pagurus acadianus

platyhelminthes platyhelminthes

Polychaeta Polychaeta

Praunus Praunus

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

sabellid sabellid

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

Semibalanus balanoides Semibalanus balanoides

Skeneopsis planorbis Skeneopsis planorbis

Spirorbis Spirorbis

Strongylocentrotus droebachiensis Strongylocentrotus droebachiensis

Tectura testinalis Tectura testinalis

Tectura testudinalis Tectura testudinalis

Thelepus cincinnatus Thelepus cincinnatus

## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?

Tonicella rubra Tonicella rubra

Turbellarid Turbellarid